improve vcf compare script
formatting
MANTA-89 comments/fluff
MANTA-89 minor pair adjustments
MANTA-89 first pieces
MANTA-89 Add Semi-mapped pairs
MANTA-89 finish trial FP filter
MANTA-89 better reference exception
MANTA-89 handle out of range ref requests in Mt
MANTA-89 allow unpaired in SVFinder